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Zinc in PDB 4xlr: Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna

Enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna

All present enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna, PDB code: 4xlr was solved by B.Bae, S.A.Darst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.56 / 4.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 289.840, 289.840, 536.340, 90.00, 90.00, 90.00
R / Rfree (%) 27.5 / 31

Other elements in 4xlr:

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna (pdb code 4xlr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna, PDB code: 4xlr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4xlr

Go back to Zinc Binding Sites List in 4xlr
Zinc binding site 1 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:0.8
occ:1.00
 SG D:CYS1112 2.2 0.8 1.0
SG D:CYS1194 2.2 0.8 1.0
SG D:CYS1201 2.3 98.3 1.0
SG D:CYS1204 2.3 0.1 1.0
NH2 D:ARG1189 2.7 0.6 1.0
CB D:CYS1201 3.1 0.2 1.0
OG1 D:THR1196 3.2 0.0 1.0
CB D:CYS1204 3.3 0.2 1.0
CB D:CYS1112 3.3 0.3 1.0
CB D:CYS1194 3.4 0.8 1.0
CA D:CYS1194 3.7 0.4 1.0
CZ D:ARG1189 4.0 0.7 1.0
N D:CYS1201 4.1 1.0 1.0
CG2 D:THR1114 4.1 0.6 1.0
N D:GLN1195 4.1 0.3 1.0
N D:CYS1112 4.1 0.0 1.0
CA D:CYS1201 4.2 0.6 1.0
CA D:CYS1112 4.4 0.3 1.0
C D:CYS1194 4.4 0.4 1.0
N D:THR1196 4.4 0.9 1.0
N D:CYS1204 4.5 0.9 1.0
CA D:CYS1204 4.5 0.8 1.0
CB D:THR1196 4.5 0.9 1.0
NE D:ARG1189 4.6 0.0 1.0
N D:CYS1194 4.9 0.7 1.0
CB D:THR1114 4.9 0.2 1.0
NH1 D:ARG1189 4.9 0.1 1.0
C D:VAL1200 5.0 0.9 1.0

Zinc binding site 2 out of 4 in 4xlr

Go back to Zinc Binding Sites List in 4xlr
Zinc binding site 2 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.6
occ:1.00
 SG D:CYS73 2.3 0.1 1.0
SG D:CYS58 2.3 0.9 1.0
SG D:CYS76 2.4 0.5 1.0
SG D:CYS60 2.4 85.0 1.0
CB D:CYS76 3.1 0.9 1.0
CB D:CYS58 3.2 0.6 1.0
CB D:CYS73 3.2 0.8 1.0
N D:CYS60 3.5 0.3 1.0
N D:ALA59 3.8 0.7 1.0
CB D:CYS60 3.9 0.6 1.0
N D:GLY61 3.9 0.0 1.0
CG D:LYS62 4.1 0.8 1.0
N D:CYS76 4.1 0.5 1.0
CA D:CYS60 4.1 0.9 1.0
N D:LYS62 4.2 0.4 1.0
CA D:CYS76 4.2 1.0 1.0
CA D:CYS58 4.4 0.2 1.0
C D:ALA59 4.4 0.9 1.0
C D:CYS58 4.4 1.0 1.0
C D:CYS60 4.5 0.0 1.0
CD2 D:TYR63 4.5 0.7 1.0
CA D:ALA59 4.6 0.8 1.0
CB D:LYS62 4.6 0.2 1.0
N D:TYR63 4.6 0.6 1.0
CA D:CYS73 4.7 0.2 1.0
C D:ARG75 4.8 0.5 1.0
CB D:ALA59 4.9 0.9 1.0
CA D:LYS62 4.9 0.8 1.0
CA D:GLY61 4.9 0.8 1.0
CB D:ARG75 4.9 0.2 1.0

Zinc binding site 3 out of 4 in 4xlr

Go back to Zinc Binding Sites List in 4xlr
Zinc binding site 3 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2001

b:0.5
occ:1.00
 SG J:CYS1112 2.2 0.8 1.0
SG J:CYS1204 2.3 0.5 1.0
SG J:CYS1194 2.3 0.7 1.0
SG J:CYS1201 2.3 1.0 1.0
NH2 J:ARG1189 2.7 0.2 1.0
CB J:CYS1201 3.1 0.3 1.0
OG1 J:THR1196 3.2 0.2 1.0
CB J:CYS1112 3.3 0.1 1.0
CB J:CYS1204 3.3 0.7 1.0
CB J:CYS1194 3.4 1.0 1.0
CA J:CYS1194 3.7 0.5 1.0
CZ J:ARG1189 4.0 0.6 1.0
CG2 J:THR1114 4.1 0.7 1.0
N J:CYS1201 4.1 0.2 1.0
N J:GLN1195 4.1 0.5 1.0
N J:CYS1112 4.1 0.5 1.0
CA J:CYS1201 4.2 0.3 1.0
CA J:CYS1112 4.4 0.1 1.0
C J:CYS1194 4.4 0.9 1.0
N J:THR1196 4.4 0.1 1.0
N J:CYS1204 4.5 0.1 1.0
CA J:CYS1204 4.5 0.1 1.0
CB J:THR1196 4.5 0.6 1.0
NE J:ARG1189 4.6 0.8 1.0
N J:CYS1194 4.9 0.8 1.0
CB J:THR1114 4.9 0.7 1.0
NH1 J:ARG1189 4.9 0.0 1.0

Zinc binding site 4 out of 4 in 4xlr

Go back to Zinc Binding Sites List in 4xlr
Zinc binding site 4 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of T.Aquaticus Transcription Initiation Complex with Card Containing Bubble Promoter and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.3
occ:1.00
 SG J:CYS60 2.3 0.1 1.0
SG J:CYS58 2.4 0.4 1.0
SG J:CYS76 2.4 0.4 1.0
SG J:CYS73 2.4 0.7 1.0
CB J:CYS76 3.0 0.5 1.0
CB J:CYS58 3.2 0.9 1.0
N J:CYS60 3.3 0.1 1.0
CB J:CYS73 3.4 0.9 1.0
CB J:CYS60 3.7 0.6 1.0
N J:ALA59 3.7 0.3 1.0
N J:GLY61 3.8 0.4 1.0
CA J:CYS60 3.9 0.3 1.0
N J:CYS76 4.1 0.6 1.0
N J:LYS62 4.2 0.2 1.0
CA J:CYS76 4.2 1.0 1.0
CG J:LYS62 4.2 0.2 1.0
C J:ALA59 4.2 0.8 1.0
C J:CYS60 4.3 0.7 1.0
C J:CYS58 4.4 0.2 1.0
CA J:CYS58 4.4 0.1 1.0
CA J:ALA59 4.4 0.5 1.0
CB J:LYS62 4.7 0.8 1.0
CB J:ALA59 4.7 0.3 1.0
N J:TYR63 4.7 0.6 1.0
CD2 J:TYR63 4.7 0.9 1.0
C J:ARG75 4.8 0.8 1.0
CA J:GLY61 4.8 0.4 1.0
CA J:CYS73 4.9 0.8 1.0
CA J:LYS62 4.9 0.7 1.0
CB J:ARG75 5.0 0.3 1.0

Reference:

B.Bae, J.Chen, E.Davis, K.Leon, S.A.Darst, E.A.Campbell. Card Uses A Minor Groove Wedge Mechanism to Stabilize the Rna Polymerase Open Promoter Complex. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26349034
DOI: 10.7554/ELIFE.08505
Page generated: Sun Oct 27 10:34:56 2024

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